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Detailed information for vg1127790146:

Variant ID: vg1127790146 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27790146
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGTAGGTGGAGGTGCATCTTCTACATTATTGAAGTGAATAGATAATCGTCGAACCTTGTCAGCAAATCTTATAGTTGCCTGTGAATGGTCTATTGCAA[T/C]
AATAAAATTCTCTTCTATTGACTTGTATGTAACAAAATTGAGTACAATATGGTGAACTACACAGGACAAAACCTCACCGCTGTCATCGATATGGACAGGC

Reverse complement sequence

GCCTGTCCATATCGATGACAGCGGTGAGGTTTTGTCCTGTGTAGTTCACCATATTGTACTCAATTTTGTTACATACAAGTCAATAGAAGAGAATTTTATT[A/G]
TTGCAATAGACCATTCACAGGCAACTATAAGATTTGCTGACAAGGTTCGACGATTATCTATTCACTTCAATAATGTAGAAGATGCACCTCCACCTACTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.20%	1.90%	4.59%	0.36%	NA
All Indica	2759	91.60%	2.10%	5.73%	0.54%	NA
All Japonica	1512	98.30%	0.60%	1.12%	0.00%	NA
Aus	269	89.60%	2.60%	7.06%	0.74%	NA
Indica I	595	89.10%	3.90%	7.06%	0.00%	NA
Indica II	465	88.20%	0.40%	9.25%	2.15%	NA
Indica III	913	96.30%	1.80%	1.86%	0.11%	NA
Indica Intermediate	786	90.10%	2.30%	7.12%	0.51%	NA
Temperate Japonica	767	98.40%	0.30%	1.30%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	95.40%	2.90%	1.66%	0.00%	NA
VI/Aromatic	96	67.70%	9.40%	22.92%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127790146	T -> DEL	LOC_Os11g45924.1	N	frameshift_variant	Average:48.567; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N
vg1127790146	T -> C	LOC_Os11g45924.1	missense_variant ; p.Ile378Val; MODERATE	nonsynonymous_codon ; I378V	Average:48.567; most accessible tissue: Minghui63 root, score: 69.344	benign	0.169	TOLERATED	0.43

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127790146	NA	4.00E-06	mr1049	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127790146	4.94E-07	1.32E-07	mr1285	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127790146	1.90E-06	1.07E-06	mr1501	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127790146	NA	7.03E-07	mr1592	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127790146	8.09E-06	3.81E-06	mr1656	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127790146	NA	6.42E-06	mr1696	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127790146	NA	1.60E-07	mr1662_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1127790146	NA	1.32E-06	mr1662_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251